- I find it very hard to get a feeling of balance, but prices seem just a little odd. I'd say that upgrades are generally too expensive; I haven't done the math, but I think that it would take some time until a 5.000 credit upgrade for a 600 credit unit pays off (lets say I research an upgrade that lets the X-Wing have 100 shield instead of 50, it costs 5.000 credits; the X-Wings that are built from now on live twice as long (about); however for 5.000 credits I could have built 10 more X-Wings (and normally upgrade don't exactly double efficiency)) Another example would be the MC120 upgrade for 60.000 credits. It's not very likely that in any normal game one builds enough MC120s for that upgrade to pay off, even if it doubles the worth of the unit.

- I also do not understand why cap ship upgrades for heroes cost that much. E.g. if I have the Emperor and 20.000 cerdits, I have the choice to either upgrade the Emperor and have a slightly better Star Destroyer, which however is linked to the Emperor and dies if he dies (in a ground battle), or I can build 2 regular Star Destroyers that can still function as a transport for his majesty. The upgrades fighter squad - cap ship are even worse, since in that case one loses a normally very good fighter unit.
IMO upgrades for heroes should cost the same or slightly less than the regular unit, since otherwise I do not know what motivation one could have for upgrading them (except of course the motivation I now have, that it's cool )

-A relatively minor issue, but my Empire AI seems to be very fond of Praetors, Skyprays and Carracks. It's kinda odd to see a Praetor in orbit of every Imperial world, but virtually no regular ISDs
-Perhaps this is only because of the AI, but bombers seem kinda overpowered. All I usually need to do as an Alliance player is build about 10 squads X-Wings and slightly upgraded Y-Wings /B-Wings later (which costs about as much as about 3-4 bigger ships) and waltz every single Imperial planet with losses of about 1 squadron per 5 planets. Again, this would maybe change if the IMP AI would mass TIE Avengers or something...

-somehow missiles/torpedos seem far too strong compared to the regular laser/ion canons. Normally a single missile can destroy an enemy fighter instantly, which means that a single squad of missile-equipped fighters can own 5 others without much trouble; at the same time, almost all cap ships I kill are destroyed before their shields are down by proton torpedos; it seems that even when attacking with Acclamators only their single proton torpedo launcher does more damage than all their laser cannons combined. Perhaps both missiles and torpedos should not ignore shields and/or shouold do relatively less damage compared to lasers and/or be limited (if thats possible code-wise)

-heroes also seem a little too expensive, considering that most of them are not much more than a slightly improved field/fleet commander and/or a fully upgraded fighters squad (e.g. a normal fleet commander gives a 25% health bonus and costs 1000 (or even 500) credits; Princess Leia does the same and gives heroes only another 25% on health and damage (I think) (so for example if I'm lucky 2 of my fighter squads are slightly better), however Leia costs 10 to 15 times what a normal fleet commander costs. This just doesn't seem right...

I hope that at least some of this is helpful. I'll play some more Empire this weekend and see if I'll get some more ideas :-)